Variant report

Variant	rs951249
Chromosome Location	chr14:64329093-64329094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:64328897-64329250	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64319483..64322302-chr14:64328481..64332813,5	MCF-7	breast:
2	chr14:64319166..64320923-chr14:64328806..64331982,4	MCF-7	breast:

Variant related genes	Relation type
SYNE2	TF binding region
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11158515	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158518	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626911	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11628650	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12161903	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12431956	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12432760	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12586461	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590842	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17750888	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17750906	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34486661	0.80[ASN][1000 genomes]
rs4899121	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902249	0.80[ASN][1000 genomes]
rs4902253	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56376318	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56401218	0.81[ASN][1000 genomes]
rs60305436	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61985718	0.80[ASN][1000 genomes]
rs61985726	0.88[ASN][1000 genomes]
rs61985748	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66460676	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66764453	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67011590	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67106029	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67975797	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140278	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143794	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145302	0.80[ASN][1000 genomes]
rs7145736	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7146469	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7149405	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7149609	0.80[ASN][1000 genomes]
rs73276854	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8008800	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8010312	0.85[ASN][1000 genomes]
rs8010385	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8013611	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8015374	0.80[ASN][1000 genomes]
rs8016321	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017009	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951250	0.80[ASN][1000 genomes]
rs998242	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64321200-64333800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:64321200-64334600	Weak transcription	Pancreas	Pancrea
3	chr14:64321200-64340600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:64321400-64330600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr14:64321400-64331200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:64321400-64350200	Weak transcription	Fetal Stomach	stomach
7	chr14:64322400-64334400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr14:64322600-64331200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:64322600-64331200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr14:64322800-64330000	Weak transcription	Fetal Kidney	kidney
11	chr14:64322800-64330000	Weak transcription	HepG2	liver
12	chr14:64322800-64330600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr14:64322800-64330800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr14:64322800-64340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:64322800-64340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:64323000-64330000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr14:64323000-64330200	Weak transcription	Primary T cells from cord blood	blood
18	chr14:64323000-64330400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:64323000-64332800	Weak transcription	Fetal Intestine Small	intestine
20	chr14:64323000-64333000	Weak transcription	Ovary	ovary
21	chr14:64323200-64331200	Weak transcription	Right Atrium	heart
22	chr14:64323200-64334400	Weak transcription	Aorta	Aorta
23	chr14:64323200-64340200	Weak transcription	Left Ventricle	heart
24	chr14:64323200-64340400	Weak transcription	Spleen	Spleen
25	chr14:64324000-64330200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr14:64324200-64329800	Weak transcription	Brain Germinal Matrix	brain
27	chr14:64324200-64330800	Weak transcription	Hela-S3	cervix
28	chr14:64324400-64329200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr14:64324400-64330800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr14:64324400-64331200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr14:64324600-64331000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr14:64324600-64331200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr14:64324600-64341400	Weak transcription	HSMM	muscle
34	chr14:64324800-64329800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr14:64324800-64330000	Weak transcription	HMEC	breast
36	chr14:64325800-64331000	Enhancers	Placenta	Placenta
37	chr14:64326600-64330800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr14:64326800-64331600	Enhancers	Stomach Mucosa	stomach
39	chr14:64327000-64330600	Enhancers	Dnd41	blood
40	chr14:64327000-64331400	Weak transcription	Thymus	Thymus
41	chr14:64327200-64331200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr14:64327200-64332000	Weak transcription	Fetal Brain Female	brain
43	chr14:64327200-64340600	Weak transcription	Right Ventricle	heart
44	chr14:64327400-64330800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr14:64327400-64330800	Weak transcription	Fetal Intestine Large	intestine
46	chr14:64327400-64331000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr14:64327400-64331000	Weak transcription	Fetal Heart	heart
48	chr14:64327400-64333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr14:64327600-64360000	Weak transcription	Gastric	stomach

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